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Switch to miniconda for build #278

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merged 3 commits into from
Mar 11, 2023
Merged

Switch to miniconda for build #278

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2e3947e
switch to miniconda for build
a-r-j Mar 11, 2023
0c50a96
update docker build
a-r-j Mar 11, 2023
8e78d45
switch to checkout v3
a-r-j Mar 11, 2023
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17 changes: 12 additions & 5 deletions .github/workflows/build.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -36,15 +36,22 @@ jobs:
# - torch: 1.9.0
# torchvision: 0.10.0
# python-version: 3.9
# https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
defaults:
run:
shell: bash -l {0}
steps:
- name: Checkout repository
uses: actions/checkout@v2
# See: https://github.com/marketplace/actions/setup-conda
- name: Setup anaconda
uses: s-weigand/setup-conda@v1
uses: actions/checkout@v3
# See: https://github.com/marketplace/actions/setup-miniconda
- name: Setup miniconda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
miniforge-variant: Mambaforge
channels: "conda-forge, salilab, pytorch, pyg"
python-version: ${{ matrix.python-version }}
conda-channels: "conda-forge, salilab, pytorch, pyg"
use-mamba: true
#- name: Set up Python ${{ matrix.python-version }}
# uses: actions/setup-python@v2
# with:
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2 changes: 1 addition & 1 deletion .github/workflows/code-style.yaml
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Expand Up @@ -9,7 +9,7 @@ jobs:

steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3

- name: Install Python
uses: actions/setup-python@v2
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18 changes: 12 additions & 6 deletions .github/workflows/code-tests-docker.yaml
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Expand Up @@ -6,17 +6,23 @@ jobs:
code-tests-docker:
name: Run code tests (docker)
runs-on: "ubuntu-latest"
defaults:
run:
shell: bash -l {0}

steps:
- name: Checkout repository
uses: actions/checkout@v2

# See: https://github.com/marketplace/actions/setup-conda
- name: Setup anaconda
uses: s-weigand/setup-conda@v1
uses: actions/checkout@v3
# See: https://github.com/marketplace/actions/setup-miniconda
- name: Setup miniconda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
miniforge-variant: Mambaforge
channels: conda-forge
python-version: 3.8
conda-channels: "conda-forge"
use-mamba: true


# # Build cache of environment
# - name: Cache conda environment
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19 changes: 13 additions & 6 deletions .github/workflows/minimal__install.yaml
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Expand Up @@ -18,19 +18,26 @@ on:
jobs:
build_cpu:
runs-on: ubuntu-latest
# https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
defaults:
run:
shell: bash -l {0}

strategy:
matrix:
python-version: [3.7, 3.8, 3.9, 3.11]
steps:
- name: Checkout repository
uses: actions/checkout@v2
# See: https://github.com/marketplace/actions/setup-conda
- name: Setup anaconda
uses: s-weigand/setup-conda@v1
uses: actions/checkout@v3
# See: https://github.com/marketplace/actions/setup-miniconda
- name: Setup miniconda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
miniforge-variant: Mambaforge
conda-channels: conda-forge
python-version: ${{ matrix.python-version }}
conda-channels: "conda-forge"

use-mamba: true
- name: Install Graphein
run: pip install -e .
- name: Install Extras
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